The Spaniard worked his way down to a 1m21.088s at the session's half-way mark - around four tenths faster than the opening session – and was never headed thereafter.
As the pace increased, so did the accidents. Gresini's Alvaro Bautista, Tech 3 Yamaha's Cal Crutchlow and Ducati's Valentino Rossi all fell – the latter bringing out the red flags as his bike pierced the air fence on the outside of Turn 3.
All were unhurt in the accidents however, and Rossi was one of the first out when the session resumed with just over 10 minutes to run.
There were to be no changes to the top order though, with Pedrosa securing top spot from Yamaha's Lorenzo and his works Honda team-mate Casey Stoner. The Honda pair found marked improvements from the morning session, while Lorenzo's gains were more modest.
Fourth to sixth didn't change from the opening practice, with Ben Spies leading the satellite Tech 3 Yamahas of Andrea Dovizioso and Cal Crutchlow.
Nicky Hayden finished as top Ducati in seventh, with LCR Honda's Stefan Bradl separating the American from team-mate Rossi. Bautista rounded out the top 10.
Friday second practice times:
1. Dani Pedrosa Honda 1m21.088s
2. Jorge Lorenzo Yamaha 1m21.422s + 0.334s
3. Casey Stoner Honda 1m21.457s + 0.369s
4. Ben Spies Yamaha 1m21.708s + 0.620s
5. Andrea Dovizioso Tech 3 Yamaha 1m22.021s + 0.933s
6. Cal Crutchlow Tech 3 Yamaha 1m22.258s + 1.170s
7. Nicky Hayden Ducati 1m22.434s + 1.346s
8. Stefan Bradl LCR Honda 1m22.568s + 1.480s
9. Valentino Rossi Ducati 1m22.772s + 1.684s
10. Alvaro Bautista Gresini Honda 1m22.853s + 1.765s
11. Aleix Espargaro Aspar Aprilia 1m23.835s + 2.747s
12. Randy de Puniet Aspar Aprilia 1m23.870s + 2.782s
13. Colin Edwards Forward Suter-BMW 1m24.732s + 3.644s
14. Toni Elias Pramac Ducati 1m24.739s + 3.651s
15. Yonny Hernandez Avintia FTR-Kawasaki 1m24.774s + 3.686s
16. Karel Abraham Cardion Ducati 1m24.849s + 3.761s
17. Mattia Pasini Speed Master Aprilia 1m25.000s + 3.912s
18. Michele Pirro Gresini FTR-Honda 1m25.065s + 3.977s
19. James Ellison Paul Bird Aprilia 1m25.166s + 4.078s
20. Ivan Silva Avintia Inmotec-Kawasaki 1m25.405s + 4.317s
21. Danilo Petrucci Ioda-Aprilia 1m25.422s + 4.334s
22. Steve Rapp Attack-Kawasaki 1m28.016s + 6.928s
- Alvaro Bautista
- Valentino Rossi